4 is actually a pretty good starting point.
If you are a somewhat serious runner, you likely have a huge advantage of beling light.
The other thing about pull ups is that being shorter than average tends to help a lot with number of reps, so if you are on the lanky side, don't feel bad that a friend you have that is built more like a wrestler or gymnast can do more in a set than you.
I'm sure that there are more scientifically proven ways to go about this, but I like to (about 3 times a week, if possible) do 3-4 sets aiming for the most total pull ups while keeping the sets pretty even (like 3 sets of 3 in your case and then if you can do that, aim for 3 sets of 4 and keep upping it from there).
changing up your grip like overhand, underhand, wide grip, etc can make things interesting.
sometimes when I'm getting back into doing pull ups and can't yet manage as many as I'd like, I'll add a few kipping pull ups at the end of my final set where i kip to get to the top, but am sure to go down very slowly to work the negative.
Another way to mix it up a little can be alternating sets of pull ups and push ups (this one saves a little time too, but I tend to take a lot of rest between sets...I'm kind of a lazy exerciser).
Be careful though. The last time I worked my way back up to being able to do over 25 pull ups in a row I would sometimes get chafing on my (rather large) lats while from running since my upper arms were rubbing against them at that point.